Plans for DEN-IM reference database update?

[Rohit-Satyam]

Hi Developers

Thanks for developing such wonderful pipeline. I saw that ViPR is now BV-BRC and have more DENV sequences 5477 genomes with 138 genomes being added (and with strain type since 2019-2022). Do you have plans to update the database? Also, will you suggest using the Asian tiger Mosquito and Yellow Fever Mosquito assemblies as well?

Request for Enhancement

We have a test MiSeq run and I observe loosing a lot of reads at trimming step. Is there a way to skip trimming and if user wish to give trimmed data as an input?

Besides I am confused regarding different type of coverage being reported by DEN-IM like integrity_coverage_1_1 and check_coverage_1_6

[cimendes]

Hello!

First of all apologies for the late reply. Regarding your question about DEN-IM's update, unfortunately, it's not on our current plans to do so. DEN-IM, although still methodologically sound, is now quite outdated, as it is still in Nextflow DLS1 and the database hasn't been updated in quite a while. I checked BV-BRC and I could not find any information regarding sero and genotype in the sequences deposited, but I'll admit that I haven't looked with much attention.

Equally, the option to skip trimming won't be implemented at the time being. Maybe adjusting the trimming parameters might help with the problem you're facing.

Regarding your question about coverage from the integrity_coverage_in_1_1 and check_coverage_1_6 processes, the first is performed on the raw read set, whereas the second is done after mapping and trimming.